title: Classification of topological domains based on gene expression and regulation.
abstract: Tissue-specific gene expression is thought to be one of the major forces shaping mammalian gene order. A recent study that used whole-genome chromosome conformation assays has shown that the mammalian genome is divided into specific topological domains that are shared between different tissues and organisms. Here, we wanted to assess whether gene expression and regulation are involved in shaping these domains and can be used to classify them. We analyzed gene expression and regulation levels in these domains by using RNA-seq and enhancer-associated ChIP-seq datasets for 17 different mouse tissues. We found 162 domains that are active (high gene expression and regulation) in all 17 tissues. These domains are significantly shorter, contain less repeats, and have more housekeeping genes. In contrast, we found 29 domains that are inactive (low gene expression and regulation) in all analyzed tissues and are significantly longer, have more repeats, and gene deserts. Tissue-specific active domains showed some correlation with tissue-type and gene ontology. Domain temporal gene regulation and expression differences also displayed some gene ontology terms fitting their temporal function. Combined, our results provide a catalog of shared and tissue-specific topological domains and suggest that gene expression and regulation could have a role in shaping them.
authors.affiliation: a Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Zhao
authors.forename: Hongbo
authors.initials: H
authors.lastname: Shi
authors.forename: Nadav
authors.initials: N
authors.lastname: Ahituv
mesh_terms: D000465:Algorithms; D000818:Animals; D047369:Chromatin Immunoprecipitation; D033481:Chromosomes, Mammalian / Q000235:genetics*; D057225:Data Mining; D015870:Gene Expression; D005786:Gene Expression Regulation; D016678:Genome; D051379:Mice; D009928:Organ Specificity; D012045:Regulatory Sequences, Nucleic Acid